To TNTCookie and anyone else who may be looking at this post in need of help
I have found the answer. It lies within the definition of a centre of mass:
$$x_{cm} = \frac{\Sigma_{i=1}^{i=N}m_i x_i}{M},$$
where $M$ is the sum of all masses in a system, and the sum in the numerator is the first moment of mass (mass moment).
If we multiply both sides of our equation by $M$, we get:
$$M\times x_{cm} = \Sigma_{i=1}^{i=N}m_i x_i.$$
This works in accordance with the steps in the MIT document as attached. We are summing individual masses multiplied by individual distances from the centre of mass. In the problem in the document, we have to deal with a lack of mass (which can be considered negative mass), and thus we get:
$$M\times |\vec{OC}| = \big(m_{\mbox{cylinder}} \times 0\big) - \big(m_{\mbox{missing cylinder}} \times \frac{R}{2}\big).$$
*Note that the distance from the centre of mass, to the centre of mass of a normal cylinder must be $0$, and the fraction $\frac{R}{2}$ comes from the problem in the attached MIT document.